🩹 Fix wrong file loading due to partial filename matching in Project

[s-weigand]

This PR fixes an issue with using project due to partial matching of file names where the wrong file was loaded if it started with the same string as the intended file, but is higher in the string sorting order.
E.g. if you had 2 files model.yml and model-target.yml in your projects models folder and would call project.load_model("model") it would load model-target.yml.
In addition, some code duplications were removed and error messages for missing files were improved.

Change summary

• 🧪 Changed project tests to fail due to partial filename matching
  (Note: The "bad" files were added to the markdown repr string since it should show all files)
• 🩹 Fix file loading
• 🧪🩹 Fixed tests that only passed due to wrong file matching
• 🧪🧹 Reduced duplication in test
• 👌 Improved error messages on file not found error

Checklist

• ✔️ Passing the tests (mandatory for all PR's)
• 🚧 Added changes to changelog (mandatory for all PR's)
• 🧪 Adds new tests for the feature (mandatory for ✨ feature and 🩹 bug fix PR's)

[github-actions]

👈 Launch a binder notebook on branch s-weigand/pyglotaran/fix-bad-file-matching-in-project

[sourcery-ai]

Sourcery Code Quality Report

❌  Merging this PR will decrease code quality in the affected files by 1.01%.

Quality metrics	Before	After	Change
Complexity	0.94 ⭐	0.96 ⭐	0.02 👎
Method Length	55.54 ⭐	56.65 ⭐	1.11 👎
Working memory	6.37 🙂	6.59 🙂	0.22 👎
Quality	78.25% ⭐	77.24% ⭐	-1.01% 👎

Other metrics	Before	After	Change
Lines	1203	1250	47

Changed files	Quality Before	Quality After	Quality Change
glotaran/project/project.py	83.50% ⭐	82.79% ⭐	-0.71% 👎
glotaran/project/project_registry.py	89.31% ⭐	89.99% ⭐	0.68% 👍
glotaran/project/project_result_registry.py	85.23% ⭐	81.61% ⭐	-3.62% 👎
glotaran/project/test/test_project.py	73.04% 🙂	72.30% 🙂	-0.74% 👎

Here are some functions in these files that still need a tune-up:

File	Function	Complexity	Length	Working Memory	Quality	Recommendation
glotaran/project/test/test_project.py	test_generate_parameters	3 ⭐	213 ⛔	9 🙂	56.54% 🙂	Try splitting into smaller methods
glotaran/project/test/test_project.py	test_missing_file_errors	0 ⭐	220 ⛔	8 🙂	61.27% 🙂	Try splitting into smaller methods
glotaran/project/test/test_project.py	test_generators_allow_overwrite	0 ⭐	151 😞	10 😞	62.82% 🙂	Try splitting into smaller methods. Extract out complex expressions
glotaran/project/test/test_project.py	test_run_optimization	2 ⭐	152 😞	8 🙂	64.98% 🙂	Try splitting into smaller methods
glotaran/project/project.py	Project.markdown	0 ⭐	78 🙂	14 😞	65.54% 🙂	Extract out complex expressions

Legend and Explanation

The emojis denote the absolute quality of the code:

• ⭐ excellent
• 🙂 good
• 😞 poor
• ⛔ very poor

The 👍 and 👎 indicate whether the quality has improved or gotten worse with this pull request.

---

Please see our documentation here for details on how these metrics are calculated.

We are actively working on this report - lots more documentation and extra metrics to come!

Help us improve this quality report!

[github-actions]

Benchmark is done. Checkout the benchmark result page.
Benchmark differences below 5% might be due to CI noise.

Benchmark diff v0.6.0 vs. main

Parametrized benchmark signatures:

BenchmarkOptimize.time_optimize(index_dependent, grouped, weight)

All benchmarks:

       before           after         ratio
     [6c3c390e]       [7dafb8f2]
     <v0.6.0>                   
!      44.7±0.2ms           failed      n/a  BenchmarkOptimize.time_optimize(False, False, False)
!      47.5±0.3ms           failed      n/a  BenchmarkOptimize.time_optimize(False, False, True)
!      44.8±0.1ms           failed      n/a  BenchmarkOptimize.time_optimize(False, True, False)
!      47.5±0.6ms           failed      n/a  BenchmarkOptimize.time_optimize(False, True, True)
!      55.3±0.3ms           failed      n/a  BenchmarkOptimize.time_optimize(True, False, False)
!       72.1±30ms           failed      n/a  BenchmarkOptimize.time_optimize(True, False, True)
!      54.8±0.2ms           failed      n/a  BenchmarkOptimize.time_optimize(True, True, False)
!        62.8±3ms           failed      n/a  BenchmarkOptimize.time_optimize(True, True, True)
             205M             209M     1.02  IntegrationTwoDatasets.peakmem_optimize
-      1.89±0.02s       1.02±0.03s     0.54  IntegrationTwoDatasets.time_optimize

Benchmark diff main vs. PR

Parametrized benchmark signatures:

BenchmarkOptimize.time_optimize(index_dependent, grouped, weight)

All benchmarks:

       before           after         ratio
     [7dafb8f2]       [3c26f363]
           failed           failed      n/a  BenchmarkOptimize.time_optimize(False, False, False)
           failed           failed      n/a  BenchmarkOptimize.time_optimize(False, False, True)
           failed           failed      n/a  BenchmarkOptimize.time_optimize(False, True, False)
           failed           failed      n/a  BenchmarkOptimize.time_optimize(False, True, True)
           failed           failed      n/a  BenchmarkOptimize.time_optimize(True, False, False)
           failed           failed      n/a  BenchmarkOptimize.time_optimize(True, False, True)
           failed           failed      n/a  BenchmarkOptimize.time_optimize(True, True, False)
           failed           failed      n/a  BenchmarkOptimize.time_optimize(True, True, True)
             209M             206M     0.99  IntegrationTwoDatasets.peakmem_optimize
       1.02±0.03s         996±20ms     0.97  IntegrationTwoDatasets.time_optimize

[codecov]

Codecov Report

Base: 87.7% // Head: 87.7% // No change to project coverage 👍

Coverage data is based on head (7dafb8f) compared to base (7dafb8f).
Patch has no changes to coverable lines.

❗ Current head 7dafb8f differs from pull request most recent head 3c26f36. Consider uploading reports for the commit 3c26f36 to get more accurate results

Additional details and impacted files

@@          Coverage Diff          @@
##            main   #1212   +/-   ##
=====================================
  Coverage   87.7%   87.7%           
=====================================
  Files        104     104           
  Lines       4968    4968           
  Branches     824     824           
=====================================
  Hits        4359    4359           
  Misses       492     492           
  Partials     117     117           

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[sonarqubecloud]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
0 Code Smells

No Coverage information
0.0% Duplication

[jsnel]

LGTM!